<tool id="ete_gene_csv_finder" name="Gene Copy Number Finder" version="@VERSION@">
    <description>from a genetree using the ETE Toolkit</description>
    <macros>
        <import>ete_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/ete_gene_cnv.py'
--genetree '$genetreeFile'
--speciesorder '$speciesorder'
> '$genes'
    ]]></command>
    <inputs>
        <param name="genetreeFile" type="data" format="nhx" label="GeneTree file" help="GeneTree in nhx format, where nodes are in form of geneid_species" />
        <param name="speciesorder" type="text" label="Species in order" help="Comma-separated species list" />
    </inputs>
    <outputs>
        <data name="genes" format="tabular" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="genetreeFile" ftype="nhx" value="test.nhx" />
            <param name="speciesorder" value="w,x,y,z,zz" />
            <output name="genes" file="test.tsv" />
        </test>
    </tests>
    <help><![CDATA[
Find copy number for genes from GeneTree by utilising the `ETE Toolkit`_. Input can be single GeneTree or multiple GeneTree in a file with one GeneTree per line.

.. _ETE Toolkit: http://etetoolkit.org/
    ]]></help>
    <expand macro="citations" />
</tool>